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Applied Microbiology and Biotechnology

, Volume 85, Issue 2, pp 207–228 | Cite as

Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches

  • Bin Cao
  • Karthiga Nagarajan
  • Kai-Chee LohEmail author
Mini-Review

Abstract

Biodegradation can achieve complete and cost-effective elimination of aromatic pollutants through harnessing diverse microbial metabolic processes. Aromatics biodegradation plays an important role in environmental cleanup and has been extensively studied since the inception of biodegradation. These studies, however, are diverse and scattered; there is an imperative need to consolidate, summarize, and review the current status of aromatics biodegradation. The first part of this review briefly discusses the catabolic mechanisms and describes the current status of aromatics biodegradation. Emphasis is placed on monocyclic, polycyclic, and chlorinated aromatic hydrocarbons because they are the most prevalent aromatic contaminants in the environment. Among monocyclic aromatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene; phenylacetic acid; and structurally related aromatic compounds are highlighted. In addition, biofilms and their applications in biodegradation of aromatic compounds are briefly discussed. In recent years, various biomolecular approaches have been applied to design and understand microorganisms for enhanced biodegradation. In the second part of this review, biomolecular approaches, their applications in aromatics biodegradation, and associated biosafety issues are discussed. Particular attention is given to the applications of metabolic engineering, protein engineering, and “omics” technologies in aromatics biodegradation.

Keywords

Biodegradation Aromatics Molecular approaches Metabolic engineering Protein engineering Omics technologies 

References

  1. Adriaens P, Focht DD (1990) Continuous coculture degradation of selected polychlorinated biphenyl congeners by Acinetobacter spp in an aerobic reactor system. Environ Sci Technol 24:1042–1049CrossRefGoogle Scholar
  2. Adrian L, Hansen SK, Fung JM, Gorisch H, Zinder SH (2007) Growth of Dehalococcoides strains with chlorophenols as electron acceptors. Environ Sci Technol 41:2318–2323CrossRefGoogle Scholar
  3. Ahamad P, Kunhi A (1996) Degradation of phenol through ortho-cleavage pathway by Pseudomonas stutzeri SPC2. Lett Appl Microbiol 22:26–29CrossRefGoogle Scholar
  4. Ahrenholtz I, Lorenz MG, Wackernagel W (1994) A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA. Appl Environ Microbiol 60:3746–3751Google Scholar
  5. Alagappan G, Cowan RM (2004) Effect of temperature and dissolved oxygen on the growth kinetics of Pseudomonas putida F1 growing on benzene and toluene. Chemosphere 54:1255–1265CrossRefGoogle Scholar
  6. Aldrich TL, Frantz B, Gill JF, Kilbane JJ, Chakrabarty AM (1987) Cloning and complete nucleotide-sequence determination of the catB gene encoding cis, cis-muconate lactonizing enzyme. Gene 52:185–195CrossRefGoogle Scholar
  7. Alvarez PJ, Vogel TM (1991) Substrate interactions of benzene, toluene, and paraxylene during microbial degradation by pure cultures and mixed culture aquifer slurries. Appl Environ Microbiol 57:2981–2985Google Scholar
  8. Amor L, Kennes C, Veiga MC (2001) Kinetics of inhibition in the biodegradation of monoaromatic hydrocarbons in presence of heavy metals. Bioresour Technol 78:181–185CrossRefGoogle Scholar
  9. Anderson RT, Lovley DR (1997) Ecology and biogeochemistry of in situ groundwater bioremediation. Adv Microb Ecol 15:289–350Google Scholar
  10. Ang EL, Zhao H, Obbard JP (2005) Recent advances in the bioremediation of persistent organic pollutants via biomolecular engineering. Enzyme Microb Technol 37:487–496CrossRefGoogle Scholar
  11. Annweiler E, Materna A, Safinowski M, Kappler A, Richnow HH, Michaelis W, Meckenstock RU (2000) Anaerobic degradation of 2-methylnaphthalene by a sulfate-reducing enrichment culture. Appl Environ Microbiol 66:5329–5333CrossRefGoogle Scholar
  12. Arias-Barrau E, Olivera ER, Luengo JM, Fernandez C, Galan B, Garcia JL, Diaz E, Minambres B (2004) The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida. J Bacteriol 186:5062–5077CrossRefGoogle Scholar
  13. Arias-Barrau E, Sandoval N, Naharro G, Olivera ER, Luengo JM (2005) A two-component hydroxylase involved in the assimilation of 3-hydroxyphenyl acetate in Pseudomonas putida. J Biol Chem 280:26435–26447CrossRefGoogle Scholar
  14. Ashok BT, Saxena S (1995) Biodegradation of polycyclic aromatic hydrocarbons—a review. J Sci Ind Res 54:443–451Google Scholar
  15. Asturias JA, Moore E, Yakimov MM, Klatte S, Timmis KN (1994) Reclassification of the polychlorinated biphenyl-degraders Acinetobacter sp strain P6 and Corynebacterium sp strain Mb1 as Rhodococcus globerulus. Syst Appl Microbiol 17:226–231Google Scholar
  16. Attaway H, Schmidt M (2002) Tandem biodegradation of BTEX components by two Pseudomonas sp. Curr Microbiol 45:30–36CrossRefGoogle Scholar
  17. Baggi G, Parbieri P, Galli E, Tollari S (1987) Isolation of a Pseudomonas stutzeri strain that degrades o-xylene. Appl Environ Microbiol 53:2129–2132Google Scholar
  18. Ball HA, Johnson HA, Reinhard M, Spormann AM (1996) Initial reactions in anaerobic ethylbenzene oxidation by a denitrifying bacterium, strain EB1. J Bacteriol 178:5755–5761Google Scholar
  19. Ballerstedt H, Hantke J, Bunge M, Werner B, Gerritse J, Andreesen JR, Lechner U (2004) Properties of a trichlorodibenzo-p-dioxin-dechlorinating mixed culture with a Dehalococcoides as putative dechlorinating species. Fems Microbiol Ecol 47:223–234CrossRefGoogle Scholar
  20. Bamforth SM, Singleton I (2005) Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions. J Chem Technol Biotechnol 80:723–736CrossRefGoogle Scholar
  21. Baraldi EA, Damianovic M, Manfio GR, Foresti E, Vazoller RF (2008) Performance of a horizontal-flow anaerobic immobilized biomass (HAIB) reactor and dynamics of the microbial community during degradation of pentachlorophenol (PCP). Anaerobe 14:268–274CrossRefGoogle Scholar
  22. Barriault D, Sylvestre M (2004) Evolution of the biphenyl dioxygenase BphA from Burkholderia xenovorans LB400 by random mutagenesis of multiple sites in region III. J Biol Chem 279:47480–47488CrossRefGoogle Scholar
  23. Beaudet R, Levesque MJ, Villemur R, Lanthier M, Chenier M, Lepine F, Bisaillon JG (1998) Anaerobic biodegradation of pentachlorophenol in a contaminated soil inoculated with a methanogenic consortium or with Desulfitobacterium frappieri strain PCP-1. Appl Microbiol Biotechnol 50:135–141CrossRefGoogle Scholar
  24. Becher D, Specht M, Hammer E, Francke W, Schauer F (2000) Cometabolic degradation of dibenzofuran by biphenyl-cultivated Ralstonia sp strain SBUG 290. Appl Environ Microbiol 66:4528–4531CrossRefGoogle Scholar
  25. Bergeron J, Ahmad D, Barriault D, Larose A, Sylvestre M, Powlowski J (1994) Identification and mapping of the gene translation products involved in the first steps of the Comamonas testosteroni B356 biphenyl chlorobiphenyl biodegradation pathway. Can J Microbiol 40:743–753Google Scholar
  26. Berka RM, Cui XJ, Yanofsky C (2003) Genomewide transcriptional changes associated with genetic alterations and nutritional supplementation affecting tryptophan metabolism in Bacillus subtilis. Proc Natl Acad Sci U S A 100:5682–5687CrossRefGoogle Scholar
  27. Bhatt P, Kumar MS, Mudliar S, Chakrabarti T (2007) Biodegradation of chlorinated compounds—a review. Crit Rev Environ Sci Technol 37:165–198CrossRefGoogle Scholar
  28. Boersma MG, Solyanikova IP, Van Berkel WJH, Vervoort J, Golovleva LA, Rietjens I (2001) F-19 NMR metabolomics for the elucidation of microbial degradation pathways of fluorophenols. J Ind Microbiol Biotechnol 26:22–34CrossRefGoogle Scholar
  29. Bouchard B, Beaudet R, Villemur R, McSween G, Lepine F, Bisaillon JG (1996) Isolation and characterization of Desulfitobacterium frappieri sp nov, an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol. Int J Syst Bacteriol 46:1010–1015Google Scholar
  30. Bouchez M, Blanchet D, Vandecasteele J-P (1995) Degradation of polycyclic aromatic hydrocarbons by pure strains and by defined strain assocciations: inhibition phenomena and cometabolism. Appl Microbiol Biotechnol 43:156–164CrossRefGoogle Scholar
  31. Bouwer EJ, Zehnder AJB (1993) Bioremediation of organic compounds—putting microbial metabolism to work. Trends Biotechnol 11:360–367CrossRefGoogle Scholar
  32. Canada KA, Iwashita S, Shim H, Wood TK (2002) Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation. J Bacteriol 184:344–349CrossRefGoogle Scholar
  33. Cerniglia C (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351–368CrossRefGoogle Scholar
  34. Chakraborty R, Coates JD (2004) Anaerobic degradation of monoaromatic hydrocarbons. Appl Microbiol Biotechnol 64:437–446CrossRefGoogle Scholar
  35. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC (1994) Green fluorescent protein as a marker for gene expression. Science 263:802–805CrossRefGoogle Scholar
  36. Chang M, Voice T, Criddle C (1993) Kinetics of competitive inhibition and cometabolism in the biodegradation of benzene, toluene, and p-xylene by two Pseudomonas isolates. Biotechnol Bioeng 41:1057–1065CrossRefGoogle Scholar
  37. Chang BV, Wu WB, Yuan SY (1997) Biodegradation of benzene, toluene, and other aromatic compounds by Pseudomonas sp. D8. Chemosphere 35:2807–2815CrossRefGoogle Scholar
  38. Chatterjee DK, Kellogg ST, Hamada S, Chakrabarty AM (1981) Plasmid specifying total degradation of 3-chlorobenzoate by a modified ortho-pathway. J Bacteriol 146:639–646Google Scholar
  39. Chen CI, Taylor RT (1995) Thermophilic biodegradation of BTEX by two Thermus species. Biotechnol Bioeng 48:614-624CrossRefGoogle Scholar
  40. Chiu TC, Yen JH, Liu TL, Wang YS (2004) Anaerobic degradation of the organochlorine pesticides DDT and heptachlor in river sediment of Taiwan. Bull Environ Contam Toxicol 72:821–828CrossRefGoogle Scholar
  41. Chung SY, Maeda M, Song E, Horikoshi K, Kudo T (1994) A Gram-positive polychlorinated biphenyl-degrading bacterium, Rhodococcus erythropolis strain Ta421, isolated from a termite ecosystem. Biosci Biotechnol Biochem 58:2111–2113CrossRefGoogle Scholar
  42. Coates JD, Chakraborty R, Lack JG, O’Connor SM, Cole KA, Bender KS, Achenbach LA (2001) Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411:1039–1043CrossRefGoogle Scholar
  43. Cobos-Vasconcelos DDL, Santoyo-Tepole F, Juarez-Ramirez C, Ruiz-Ordaz N, Galindez-Mayer CJJ (2006) Cometabolic degradation of chlorophenols by a strain of Burkholderia in fed-batch culture. Enzyme Microb Technol 40:57–60CrossRefGoogle Scholar
  44. Committee on the Biological Confinement of Genetically Engineered Organisms (2004) Biological confinement of genetically engineered organisms. The National Academies Press, Washington DCGoogle Scholar
  45. Contreras A, Molin S, Ramos JL (1991) Conditional suicide containment system for bacteria which mineralize aromatics. Appl Environ Microbiol 57:1504–1508Google Scholar
  46. Davey M, O’Toole G (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev 64:847–867CrossRefGoogle Scholar
  47. Dean-Ross D, Moody J, Freeman J, Doerge D, Cerniglia C (2001) Metabolism of anthracene by a Rhodococcus species. FEMS Microbiol Lett 204:205–211CrossRefGoogle Scholar
  48. Deeb R, Cohen L (1999) Temperature effects and substrate interactions during the aerobic transformation of BTEX mixtures by toluene enriched consortia and Rhodococcus rhodochrous. Biotechnol Bioeng 62:526–536CrossRefGoogle Scholar
  49. Deeb R, Cohen L (2000) Aerobic transformation of gasoline aromatics in multicomponent mixtures. Bioremed J 4:1–9CrossRefGoogle Scholar
  50. Delawary M, Ohtsubo Y, Ohta A (2003) The dual functions of biphenyl-degrading ability of Pseudomonas sp KKS102: energy acquisition and substrate detoxification. Biosci Biotechnol Biochem 67:1970–1975CrossRefGoogle Scholar
  51. Demir G (2004) Degradation of toluene and benzene by Trametes versicolor. J Environ Biol 25:19–25CrossRefGoogle Scholar
  52. Denef VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM (2004) Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70:4961–4970CrossRefGoogle Scholar
  53. Dennis JJ (2005) The evolution of IncP catabolic plasmids. Curr Opin Biotechnol 16:291–298CrossRefGoogle Scholar
  54. Deweerd KA, Suflita JM (1990) Anaerobic aryl reductive dehalogenation of halobenzoates by cell extracts of Desulfomonile tiedjei. Appl Environ Microbiol 56:2999–3005Google Scholar
  55. Diaz E (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int Microbiol 7:173–180Google Scholar
  56. Diaz E, Prieto MA (2000) Bacterial promoters triggering biodegradation of aromatic pollutants. Curr Opin Biotechnol 11:467–475CrossRefGoogle Scholar
  57. Diels L, Mergeay M (1990) DNA probe-mediated detection of resistant bacteria from soils highly pollutied by heavy metals. Appl Environ Microbiol 56:1485–1491Google Scholar
  58. DiGioia D, Sciubba L, Bertin L, Barberio C, Salvadori L, Frassinetti S, Fava F (2009) Nonylphenol polyethoxylate degradation in aqueous waste by the use of batch and continuous biofilm bioreactors. Water Res 43:2977–2988CrossRefGoogle Scholar
  59. Dominguez-Cuevas P, Gonzalez-Pastor JE, Marques S, Ramos JL, de Lorenzo V (2006) Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J Biol Chem 281:11981–11991CrossRefGoogle Scholar
  60. Duetz W, de Jong C, Williams P, van Andel JG (1994) Competition in chemostat culture between Pseudomonas strains that use different pathways for the degradation of toluene. Appl Environ Microbiol 60:2858–2863Google Scholar
  61. Duhamel M, Mo K, Edwards EA (2004) Characterization of a highly enriched Dehalococcoides-containing culture that grows on vinyl chloride and trichloroethene. Appl Environ Microbiol 70:5538–5545CrossRefGoogle Scholar
  62. Elasri M, Miller R (1999) Study of the response of a biofilm bacterial community to UV radiation. Appl Environ Microbiol 65:2025–2031Google Scholar
  63. Eriksson M, Sodersten E, Yu ZT, Dalhammar G, Mohn WW (2003) Degradation of polycyclic aromatic hydrocarbons at low temperature under aerobic and nitrate-reducing conditions in enrichment cultures from northern soils. Appl Environ Microbiol 69:275–284CrossRefGoogle Scholar
  64. Estevez E, Veiga MC, Kennes C (2005) Biodegradation of toluene by the new fungal isolates Paecilomyces variotii and Exophiala oligosperma. J Ind Microbiol Biotechnol 32:33–37CrossRefGoogle Scholar
  65. Farhadian M, Duchez D, Vachelard C, Larroche C (2008) Monoaromatics removal from polluted water through bioreactors—a review. Water Res 42:1325–1341CrossRefGoogle Scholar
  66. Feitkenhauer H, Muller R, Markl H (2003) Degradation of polycyclic aromatic hydrocarbons and long chain alkanes at 60–70°C by Thermus and Bacillus spp. Biodegradation 14:367–372CrossRefGoogle Scholar
  67. Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E (1998) Catabolism of phenylacetic acid in Escherichia coli—characterization of a new aerobic hybrid pathway. J Biol Chem 273:25974–25986CrossRefGoogle Scholar
  68. Garcia B, Olivera ER, Minambres B, Fernandez-Valverde M, Canedo LM, Prieto MA, Garcia JL, Martinez M, Luengo JM (1999) Novel biodegradable aromatic plastics from a bacterial source—genetic and biochemical studies on a route of the phenylacetyl-CoA catabolon. J Biol Chem 274:29228–29241CrossRefGoogle Scholar
  69. Gerritse J, Renard V, Gomes TMP, Lawson PA, Collins MD, Gottschal JC (1996) Desulfitobacterium sp strain PCE1, an anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethene or ortho-chlorinated phenols. Arch Microbiol 165:132–140CrossRefGoogle Scholar
  70. Ghazali F, Rahman R, Salleh A, Basari M (2004) Biodegradation of hydrocarbons in soil by microbial consortium. Int Biodeterior Biodegrad 54:61–67CrossRefGoogle Scholar
  71. Goncalves ER, Hara H, Miyazawa D, Davies JE, Eltis LD, Mohn WW (2006) Transcriptomic assessment of isozymes in the biphenyl pathway of Rhodococcus sp strain RHA1. Appl Environ Microbiol 72:6183–6193CrossRefGoogle Scholar
  72. Gonzalez G, Herrera G, Garcia MT, Pena M (2001) Biodegradation of phenolic industrial wastewater in a fluidized bed reactor with immobilized cells of Pseudomonas putida. Bioresour Technol 80:137–142CrossRefGoogle Scholar
  73. Goris J, De Vos P, Caballero-Mellado J, Park J, Falsen E, Quensen JF, Tiedje JM, Vandamme P (2004) Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400 and relatives as Burkholderia xenovorans sp nov. Int J Syst Evol Microbiol 54:1677–1681CrossRefGoogle Scholar
  74. Gulensory N, Alvarez P (1999) Diversity and correlation of specific aromatic hydrocarbon biodegradation capabilities. Biodegradation 10:331–340CrossRefGoogle Scholar
  75. Harms G, Zengler K, Rabus R, Aeckersberg F, Minz D, Rossello-Mora R, Widdel F (1999) Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Appl Environ Microbiol 65:999–1004Google Scholar
  76. Haro MA, de Lorenzo V (2001) Metabolic engineering of bacteria for environmental applications: construction of Pseudomonas strains for biodegradation of 2-chlorotoluene. J Biotechnol 85:103–113CrossRefGoogle Scholar
  77. Harwood CS, Parales RE (1996) The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50:553–590CrossRefGoogle Scholar
  78. Henikoff S, Haughn GW, Calvo JM, Wallace JC (1988) A large family of bacterial activator proteins. Proc Natl Acad Sci U S A 85:6602–6606CrossRefGoogle Scholar
  79. Hermann H, Muller C, Schmidt I, Mahnke J, Petruschka L, Hahnke K (1995) Localization and organization of phenol degradation genes of Pseudomonas strain H. Mol Gen Genet 247:240–246CrossRefGoogle Scholar
  80. Hess A, Zarda B, Hahn D, Haner A, Stax D, Hohener P, Zeyer J (1997) In situ analysis of denitrifying toluene- and m-xylene-degrading bacteria in a diesel fuel-contaminated laboratory aquifer column. Appl Environ Microbiol 63:2136–2141Google Scholar
  81. Hickey WJ, Sabat G, Yuroff AS, Arment AR, Perez-Lesher J (2001) Cloning, nucleotide sequencing, and functional analysis of a novel, mobile cluster of biodegradation genes from Pseudomonas aeruginosa strain JB2. Appl Environ Microbiol 67:4603–4609CrossRefGoogle Scholar
  82. Hoffmann D, Kleinsteuber S, Muller RH, Babel W (2003) A transposon encoding the complete 2, 4-dichlorophenoxyacetic acid degradation pathway in the alkalitolerant strain Delftia acidovorans P4a. Microbiology 149:2545–2556CrossRefGoogle Scholar
  83. Hollywood K, Brison DR, Goodacre R (2006) Metabolomics: current technologies and future trends. Proteomics 6:4716–4723CrossRefGoogle Scholar
  84. Hrywna Y, Tsoi TV, Maltseva OV, Quensen JF, Tiedje JM (1999) Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. Appl Environ Microbiol 65:2163–2169Google Scholar
  85. Jeon CO, Park W, Padmanabhan P, DeRito C, Snape JR, Madsen EL (2003) Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc Natl Acad Sci U S A 100:13591–13596CrossRefGoogle Scholar
  86. Juang RS, Kao HC (2009) Estimation of the contribution of immobilized biofilm and suspended biomass to the biodegradation of phenol in membrane contactors. Biochem Eng J 43:122–128CrossRefGoogle Scholar
  87. Juang RS, Wu CY (2007) Microbial degradation of phenol in high-salinity solutions in suspensions and hollow fiber membrane contactors. Chemosphere 66:191–198CrossRefGoogle Scholar
  88. Jung IG, Park CH (2004) Characteristics of Rhodococcus pyridinovorans PYJ-1 for the biodegradation of benzene, toluene, m-xylene (BTX), and their mixtures. J Biosci Bioeng 97:429–431Google Scholar
  89. Kang DG, Choi SS, Cha HJ (2006) Enhanced biodegradation of toxic organophosphate compounds using recombinant Escherichia coli with sec pathway-driven periplasmic secretion of organophosphorus hydrolase. Biotechnol Prog 22:406–410CrossRefGoogle Scholar
  90. Kang E, Oh JM, Lee J, Kim YC, Min KH, Min KR, Kim Y (1998) Genetic structure of the bphG gene encoding 2-hydroxymuconic semialdehyde dehydrogenase of Achromobacter xylosoxidans KF701. Biochem Biophys Res Commun 246:20–25CrossRefGoogle Scholar
  91. Keenan BG, Leungsakul T, Smets BF, Wood TK (2004) Saturation mutagenesis of Burkholderia cepacia R34 2, 4-dinitrotoluene dioxygenase at DntAc valine 350 for synthesizing nitrohydroquinone, methylhydroquinone, and methoxyhydroquinone. Appl Environ Microbiol 70:3222–3231CrossRefGoogle Scholar
  92. Kelley I, Freeman JP, Cerniglia CE (1990) Identification of metabolites from degradation of naphthalene by a Mycobacterium sp. Biodegradation 1:283–290CrossRefGoogle Scholar
  93. Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C (2000) DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc Natl Acad Sci U S A 97:12170–12175CrossRefGoogle Scholar
  94. Khomenkov V, Shevelev A, Zhukov V, Zagustina N, Bezborodov A, Popov V (2008) Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic degradation in microorganisms: a review. Appl Biochem Microbiol 44:117–135Google Scholar
  95. Kim J, Jeon C (2009) Isolation and characterization of a new benzene, toluene, and ethylbenzene degrading bacterium, Acinetobacter sp. B113. Curr Microbiol 58:70–75CrossRefGoogle Scholar
  96. Kim JM, Le NT, Chung BS, Park JH, Bae JW, Madsen EL, Jeon CO (2008) Influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BDa59. Appl Environ Microbiol 74:7313–7320CrossRefGoogle Scholar
  97. Kim D, Kim Y, Kim S, Kim S, Zylstra G, Kim Y, Kim E (2002) Monocyclic aromatic hydrocarbon degradation by Rhodococcus sp. strain DK17. Appl Environ Microbiol 68:3270–3278CrossRefGoogle Scholar
  98. Kim S, Kweon O, Cerniglia C (2009) Proteomic applications to elucidate bacterial aromatic hydrocarbon metabolic pathways. Curr Opin Microbiol 12:1–9CrossRefGoogle Scholar
  99. Kuhner S, Wohlbrand L, Fritz I, Wruck W, Hultschig C, Hufnagel P, Kube M, Reinhardt R, Rabus R (2005) Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 187:1493–1503CrossRefGoogle Scholar
  100. Lee J, Roh J, Kim H (1993) Metabolic engineering of Pseudomonas putida for the simultaneous biodegradation of benzene, toluene, and p-xylene mixture. Biotechnol Bioeng 43:1146–1152CrossRefGoogle Scholar
  101. Lee J, Jung K, Choi S, Kim H (1995) Combination of the tod and the tol pathways in redesigning a metabolic route of Pseudomonas putida for the mineralization of a benzene, toluene, and p-xylene mixture. Appl Environ Microbiol 61:2211–2217Google Scholar
  102. Lee S, Lee S (2001) Isolation and characterization of a thermotolerant bacterium Ralstonia sp. strain PHS1 that degrades benzene, toluene, ethyl benzene and o-xylene. Appl Environ Microbiol 56:270–275Google Scholar
  103. Li Y, Loh KC (2006a) Activated carbon impregnated polysulfone hollow fiber membrane for cell immobilization and cometabolic biotransformation of 4-chlorophenol in the presence of phenol. J Membr Sci 276:81–90CrossRefGoogle Scholar
  104. Li Y, Loh KC (2006b) Continuous cometabolic transformation of 4-chlorophenol in the presence of phenol in a hollow fiber membrane bioreactor. J Environ Eng-ASCE 132:309–314CrossRefGoogle Scholar
  105. Li H, Liu YH, Luo N, Zhang XY, Luan TG, Hu JM, Wang ZY, Wu PC, Chen MJ, Lu JQ (2006) Biodegradation of benzene and its derivatives by a psychrotolerant and moderately haloalkaliphilic Planococcus sp. strain ZD22. Res Microbiol 157:629–636CrossRefGoogle Scholar
  106. Lindow SE (1995) The use of reporter genes in the study of microbial ecology. Mol Ecol 4:555–566CrossRefGoogle Scholar
  107. Linkfield TG, Tiedje JM (1990) Characterization of the requirements and substrates for reductive dehalogenation by strain DCB-1. J Ind Microbiol 5:9–16CrossRefGoogle Scholar
  108. Liu S, Ogawa N, Miyashita K (2001) The chlorocatechol degradative genes, tfdT-CDEF, of Burkholderia sp strain NK8 are involved in chlorobenzoate degradation and induced by chlorobenzoates and chlorocatechols. Gene 268:207–214CrossRefGoogle Scholar
  109. Loh K, Cao B (2008) Paradigm in biodegradation using Pseudomonas putida—a review of proteomics studies. Enzyme Microb Technol 43:1–12CrossRefGoogle Scholar
  110. Loh KC, Ranganath S (2005) External-loop fluidized bed airlift bioreactor (EFBAB) for the cometabolic biotransformation of 4-chlorophenol (4-cp) in the presence of phenol. Chem Eng Sci 60:6313–6319CrossRefGoogle Scholar
  111. Loh KC, Wang Y (2006) Enhanced cometabolic transformation of 4-chlorophenol in the presence of phenol by granular activated carbon adsorption. Can J Chem Eng 84:248–255Google Scholar
  112. Loh KC, Wu TT (2006) Cometabolic transformation of 2-chlorophenol and 4-chlorophenol in the presence of phenol by Pseudomonas putida. Can J Chem Eng 84:356–367CrossRefGoogle Scholar
  113. Lovley DR, Baedecker MJ, Lonergan DJ, Cozzarelli IM, Phillips EJP, Siegel DI (1989) Oxidation of aromatic contaminants coupled to microbial iron reduction. Nature 339:297–300CrossRefGoogle Scholar
  114. Luengo J, Arias S, Arcos M, Olivera E (2007) The catabolism of phenylacetic acid and other related molecules in Pseudomonas putida U in Pseudomonas: a model system in biology edited by Ramos J. Springer, Filloux AGoogle Scholar
  115. Luengo JM, Garcia JL, Olivera ER (2001) The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications. Mol Microbiol 39:1434–1442CrossRefGoogle Scholar
  116. Lundstedt S, Haglund P, Oberg L (2003) Degradation and formation of polycyclic aromatic compounds during bioslurry treatment of an acid aged gasworks soil. Environ Toxicol Chem 22:1413–1420CrossRefGoogle Scholar
  117. Lunt D, Evans WC (1970) The microbial metabolism of biphenyl. Biochem J 118:54–55Google Scholar
  118. Meckenstock RU, Annweiler E, Michaelis W, Richnow HH, Schink B (2000) Anaerobic naphthalene degradation by a sulphate-reducing enrichment culture. Appl Environ Microbiol 66:2743–2747CrossRefGoogle Scholar
  119. Meckenstock RU, Safinowski M, Griebler C (2004) Anaerobic degradation of polycyclic aromatic hydrocarbons. Fems Microbiol Ecol 49:27–36CrossRefGoogle Scholar
  120. Meyer A, Held M, Schmid A, Kohler HPE, Witholt B (2003) Synthesis of 3-tert-butylcatechol by an engineered monooxygenase. Biotechnol Bioeng 81:518–524CrossRefGoogle Scholar
  121. Minambres B, MartinezBlanco H, Olivera ER, Garcia B, Diez B, Barredo JL, Moreno MA, Schleissner C, Salto F, Luengo JM (1996) Molecular cloning and expression in different microbes of the DNA encoding Pseudomonas putida U phenylacetyl-CoA ligase—use of this gene to improve the rate of benzylpenicillin biosynthesis in Penicillium chrysogenum. J Biol Chem 271:33531–33538CrossRefGoogle Scholar
  122. Mishra V, Lal R, Srinivasan (2001) Enzymes and operons mediating xenobiotic degradation in bacteria. Crit Rev Microbiol 27:133–166Google Scholar
  123. Mitchell K, Studts J, Fox B (2002) Combined participation of hydroxylase active site residues and effector protein binding in a para to ortho modulation of toluene 4-monooxygenase regiospecificity. Biochemistry 41:3176–3188CrossRefGoogle Scholar
  124. Mohn WW, Kennedy KJ (1992) Reductive dehalogenation of chlorophenols by Desulfomonile tiedjei DCB-1. Appl Environ Microbiol 58:1367–1370Google Scholar
  125. Mohn WW, Tiedje JM (1992) Microbial reductive dehalogenation. Microbiol Rev 56:482–507Google Scholar
  126. Moiseeva OV, Solyanikova IP, Kaschabek SR, Groning J, Thiel M, Golovleva LA, Schlomann M (2002) A new modified ortho cleavage pathway of 3-chlorocatechol degradation by Rhodococcus opacus 1CP: genetic and biochemical evidence. J Bacteriol 184:5282–5292CrossRefGoogle Scholar
  127. Molin S, Boe L, Jensen LB, Kristensen CS, Givskov M, Ramos JL, Bej AK (1993) Suicidal genetic elements and their use in biological containment of bacteria. Annu Rev Microbiol 47:139–166CrossRefGoogle Scholar
  128. Monds R, O’Toole G (2009) The developmental model of microbial biofilms: ten years of a paradigm up for review. Trends Microbiol 17:73–87CrossRefGoogle Scholar
  129. Monti MR, Smania AM, Fabro G, Alvarez ME, Argarana CE (2005) Engineering Pseudomonas fluorescens for biodegradation of 2,4-dinitrotoluene. Appl Environ Microbiol 71:8864–8872CrossRefGoogle Scholar
  130. Moody J, Freeman J, Doerge D, Cerniglia C (2001) Degradation of phenanthrene and anthracene by cell suspensions of Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67:1476–1483CrossRefGoogle Scholar
  131. Moon J, Kang E, Min KR, Kim CK, Min KH, Lee KS, Kim Y (1997) Characterization of the gene encoding catechol 2,3-dioxygenase from Achromobacter xylosoxidans KF701. Biochem Biophys Res Commun 238:430–435CrossRefGoogle Scholar
  132. Muller JA, Rosner BM, von Abendroth G, Meshulam-Simon G, McCarty PL, Spormann AM (2004) Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp strain VS and its environmental distribution. Appl Environ Microbiol 70:4880–4888CrossRefGoogle Scholar
  133. Nicolella C, Zolezzi M, Furfaro M, Cattaneo C, Rovatti M (2007) High-rate degradation of aromatic sulfonates in a biofilm airlift suspension reactor. Ind Eng Chem Res 46:6674–6680CrossRefGoogle Scholar
  134. Nilotpala P, Ingle A (2003) Degradation of phenol through ortho pathway by Pseudomonas sp. BC1. Indian J Microbiol 43:267–269Google Scholar
  135. Ogawa N, Miyashita K (1999) The chlorocatechol-catabolic transposon Tn5707 of Alcaligenes eutrophus NH9, carrying a gene cluster highly homologous to that in the 1,2,4-trichlorobenzene-degrading bacterium Pseudomonas sp. strain P51, confers the ability to grow on 3-chlorobenzoate. Appl Environ Microbiol 65:724–731Google Scholar
  136. Oh Y, Bartha R (1997) Construction of a bacterial consortium for the biofiltration of benzene, toluene and xylene emission. World J Microbiol Biotechnol 13:627–632CrossRefGoogle Scholar
  137. Oh Y, Sharafdeen Z, Baltizs B, Bartha R (1994) Interactions between benzene, toluene, and p-xylene (BTX) during their biodegradation. Biotechnol Bioeng 44:533–538CrossRefGoogle Scholar
  138. Ohtsubo Y, Shimura M, Delawary M, Kimbara K, Takagi M, Kudo T, Ohta A, Nagata Y (2003) Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: promoter implantation by homologous recombination. Appl Environ Microbiol 69:146–153CrossRefGoogle Scholar
  139. Okuta A, Ohnishi K, Harayama S (2004) Construction of chimeric catechol 2,3-dioxygenase exhibiting improved activity against the suicide inhibitor 4-methylcatechol. Appl Environ Microbiol 70:1804–1810CrossRefGoogle Scholar
  140. Olivera ER, Minambres B, Garcia B, Muniz C, Moreno MA, Ferrandez A, Diaz E, Garcia JL, Luengo JM (1998) Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon. Proc Natl Acad Sci U S A 95:6419–6424CrossRefGoogle Scholar
  141. Parales RE, Ditty JL, Harwood CS (2000) Toluene-degrading bacteria are chemotactic towards the environmental pollutants benzene, toluene, and trichloroethylene. Appl Environ Microbiol 66:4098–4104CrossRefGoogle Scholar
  142. Parsek MR, Ye RW, Pun P, Chakrabarty AM (1994) Critical nucleotides in the interaction of a Lysr-type regulator with its target promoter region—CatBC promoter activation by CatR. J Biol Chem 269:11279–11284Google Scholar
  143. Pieper DH (2005) Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol 67:170–191CrossRefGoogle Scholar
  144. Poh RPC, Smith ARW, Bruce IJ (2002) Complete characterisation of Tn5530 from Burkholderia cepacia strain 2a (pIJB1) and studies of 2,4-dichlorophenoxyacetate uptake by the organism. Plasmid 48:1–12CrossRefGoogle Scholar
  145. Polen I, Kramer A, Bongaerts J, Wubbolts M, Wendisch VF (2005) The global gene expression response of Escherichia coli to L-phenylalanine. J Biotechnol 115:221–237CrossRefGoogle Scholar
  146. Pollmann K, Wray V, Hecht HJ, Pieper DH (2003) Rational engineering of the regioselectivity of TecA tetrachlorobenzene dioxygenase for the transformation of chlorinated toluenes. Microbiology 149:903–913CrossRefGoogle Scholar
  147. Potrawfke T, Armengaud J, Wittich RM (2001) Chlorocatechols substituted at positions 4 and 5 are substrates of the broad-spectrum chlorocatechol 1,2-dioxygenase of Pseudomonas chlororaphis RW71. J Bacteriol 183:997–1011CrossRefGoogle Scholar
  148. Prosser JI, Killham K, Glover LA, Rattray EAS (1996) Luminescence-based systems for detection of bacteria in the environment. Crit Rev Biotechnol 16:157–183CrossRefGoogle Scholar
  149. Prenafeta-Boldu FX, Vervoort J, Grotenhuis JTC, van Groenestijn (2002) Substrate interactions during the biodegradation of benzene, toluene, ethylbenzene, and xylene (BTEX) hydrocarbons by the fugus Cladophialophora sp. strain T1. Appl Environ Microbiol 68:2660–2665Google Scholar
  150. Rabus R, Widdel F (1995) Anaerobic degradation of ethylbenzene and other aromatic-hydrocarbons by new denitrifying bacteria. Arch Microbiol 163:96–103CrossRefGoogle Scholar
  151. Reardon KF, Mosteller DC, Rogers JB (2000) Biodegradation kinetics of benzene, toluene, and phenol as single and mixed substrates for Pseudomonas putida F1. Biotechnol Bioeng 69:385–400CrossRefGoogle Scholar
  152. Reardon K, Mosteller D, Rogers J, Du Teau N, Hong K (2002) Biodegradation kinetics of aromatic hydrocarbon mixtures by pure and mixed bacterial cultures. Environ Health Perspect 110:1005–1011Google Scholar
  153. Reineke W (1998) Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly. Annu Rev Microbiol 52:287–331CrossRefGoogle Scholar
  154. Reva ON, Weinel C, Weinel M, Bohm K, Stjepandic D, Hoheisel JD, Tummler B (2006) Functional genomics of stress response in Pseudomonas putida KT2440. J Bacteriol 188:4079–4092CrossRefGoogle Scholar
  155. Rhee SK, Liu XD, Wu LY, Chong SC, Wan XF, Zhou JZ (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303–4317CrossRefGoogle Scholar
  156. Rivas I, Arvin E (2000) Biodegradation of thiophene by cometabolism in a biofilm system. Water Sci Technol 41:461–468Google Scholar
  157. Rockne KJ, Chee-Sanford JC, Sanford RA, Hedlund BP, Staley JT, Strand SE (2000) Anaerobic naphthalene degradation by microbial pure cultures under nitrate-reducing conditions. Appl Environ Microbiol 66:1595–1601CrossRefGoogle Scholar
  158. Rogers JB, Reardon KF (2000) Modeling substrate interactions during the biodegradation of mixtures of toluene and phenol by Burkholderia species JS150. Biotechnol Bioeng 70:428–435CrossRefGoogle Scholar
  159. Rooney-Varga JN, Anderson RT, Fraga JL, Ringelberg D, Lovley DR (1999) Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl Environ Microbiol 65:3056–3063Google Scholar
  160. Rui LY, Kwon YM, Fishman A, Reardon KF, Wood TK (2004) Saturation mutagenesis of toluene ortho-monooxygenase of Burkholderia cepacia G4 for enhanced 1-naphthol synthesis and chloroform degradation. Appl Environ Microbiol 70:3246–3252CrossRefGoogle Scholar
  161. Ruppe S, Neumann A, Vetter W (2003) Anaerobic transformation of compounds of technical toxaphene. I. Regiospecific reaction of chlorobornanes with geminal chlorine atoms. Environ Toxicol Chem 22:2614–2621CrossRefGoogle Scholar
  162. Ruppe S, Neumann A, Braekevelt E, Tomy GT, Stern GA, Maruya KA, Vetter W (2004) Anaerobic transformation of compounds of technical toxaphene. 2. Fate of compounds lacking geminal chlorine atoms. Environ Toxicol Chem 23:591–598CrossRefGoogle Scholar
  163. Saagua MC, Vieira G, Paveia H, Anselmo A (1998) Isolation and preliminary characterization of Bacillus sp. MCS, a Gram-positive 4-chlorobiphenyl degrading bacterium. Int Biodeterior Biodegrad 42:39–43CrossRefGoogle Scholar
  164. Sanford RA, Cole JR, Loffler FE, Tiedje JN (1996) Characterization of Desulfitobacterium chlororespirans sp nov, which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate. Appl Environ Microbiol 62:3800–3808Google Scholar
  165. Sanford RA, Cole JR, Tiedje JM (2002) Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol 68:893–900CrossRefGoogle Scholar
  166. Sariaslani F, Harper D, Higgins I (1974) Microbial degradation of hydrocarbons: catabolism of 1-phenylalkanes by Nocardia salmonicolor. Biochem J 140:31–45Google Scholar
  167. Sayler GS, Ripp S (2000) Field applications of genetically engineered microorganisms for bioremediation processes. Curr Opin Biotechnol 11:286–289CrossRefGoogle Scholar
  168. Shelton DR, Tiedje JM (1984) Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic acid. Appl Environ Microbiol 48:840–848Google Scholar
  169. Shim H, Shin EB, Yang ST (2002) A continuous fibrous-bed bioreactor for BTEX biodegradation by a co-culture of Pseudomonas putida and Pseudomonas fluorescens. Adv Environ Res 7:203-216CrossRefGoogle Scholar
  170. Shimura M, Mukerjee-Dhar G, Kimbara K, Nagato H, Kiyohara H, Hatta T (1999) Isolation and characterization of a thermophilic Bacillus sp JF8 capable of degrading polychlorinated biphenyls and naphthalene. FEMS Microbiol Lett 178:87–93CrossRefGoogle Scholar
  171. Shuttleworth K, Cerniglia C (1995) Environmental aspects of PAH biodegradation. Appl Biochem Biotechnol 54:291–302CrossRefGoogle Scholar
  172. Singh R, Paul D, Jain RK (2006) Biofilms: implications in bioremediation. Trends Microbiol 14:389–397CrossRefGoogle Scholar
  173. Singh S, Kang S, Mulchandani A, Chen W (2008) Bioremediation: environmental clean-up through pathway engineering. Curr Opin Biotechnol 19:437–444CrossRefGoogle Scholar
  174. Stephenson J, Warnes A (1996) Release of genetically modified micro-organisms into the environment. J Chem Technol Biotechnol 65:5–14CrossRefGoogle Scholar
  175. Stoecker MA, Herwig RP, Staley JT (1994) Rhodococcus zopfii sp. nov., a toxicantdegrading bacterium. Int J Syst Bacteriol 44:106–110CrossRefGoogle Scholar
  176. Suyama A, Iwakiri R, Kimura N, Nishi A, Nakamura K, Furukawa K (1996) Engineering hybrid Pseudomonads capable of utilizing a wide range of aromatic hydrocarbons and of efficient degradation of trichloroethylene. J Bacteriol 178:4039–4046Google Scholar
  177. Tabak H, Lazorchak J, Lei L, Khodadoust A, Antia J, Bagchi R, Suidan M (2003) Studies on bioremediation of polycyclic aromatic hydrocarbon-contaminated sediments: bioavailability, biodegradability, and toxicity issues. Environ Toxicol Chem 22:473–482CrossRefGoogle Scholar
  178. Tao Y, Fishman A, Bentley W, Wood T (2004) Oxidation of benzene to phenol, catechol, and 1,2,3-trihydroxybenzene by toluene 4-monooxygenase of Pseudomonas mendocina KR-1 and toluene 3-monooxygenase of Ralstonia pickettii PKO1. Appl Environ Microbiol 70:3814–3820CrossRefGoogle Scholar
  179. Tartakovsky B, Levesque MJ, Dumortier R, Beaudet R, Guiot SR (1999) Biodegradation of pentachlorophenol in a continuous anaerobic reactor augmented with Desulfitobacterium frappieri PCP-1. Appl Environ Microbiol 65:4357–4362Google Scholar
  180. Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Perez-Pantoja D, Sanchez MA, Stuardo M, Gonzalez B (2004) Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol 6:655–668CrossRefGoogle Scholar
  181. Tropel D, van der Meer JR (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68:474–500CrossRefGoogle Scholar
  182. Vainberg S, Togna AP, Sutton PM, Steffan RJ (2002) Treatment of MTBEcontaminated water in fluidized bed bioreactor. J Environ Eng 128:842-851CrossRefGoogle Scholar
  183. van Herwijnen R, Springael D, Slot P, Govers HAJ, Parsons JR (2003a) Degradation of anthracene by Mycobacterium sp strain LB501T proceeds via a novel pathway, through o-phthalic acid. Appl Environ Microbiol 69:186–190CrossRefGoogle Scholar
  184. van Herwijnen R, Wattiau P, Bastiaens L, Daal L, Jonker L, Springael D, Govers HAJ, Parsons JR (2003b) Elucidation of the metabolic pathway of fluorene and cometabolic pathways of phenanthrene, fluoranthene, anthracene and dibenzothiophene by Sphingomonas sp LB126. Res Microbiol 154:199–206CrossRefGoogle Scholar
  185. Vandentweel WJJ, Smits JP, Debont JAM (1988) Catabolism of DL-alpha-phenylhydracrylic, phenylacetic and 3-hydroxyphenylacetic and 4-hydrophenylacetic acid via homogentisate acid in a Flavobacterium sp. Arch Microbiol 149:207–213CrossRefGoogle Scholar
  186. Vandermeer JR, Vanneerven ARW, Devries EJ, Devos WM, Zehnder AJB (1991) Cloning and characterization of plasmid-encoded genes for the degradation of 1,2-dichlorobenzene, 1,4-dichlorobenzene, and 1,2,4-trichlorobenzene of Pseudomonas sp strain P51. J Bacteriol 173:6–15Google Scholar
  187. Vasudevan N, Mahadevan A (1992) Utilization of complex phenolic compounds by Acinetobacter sp. Appl Microbiol Biotechnol 37:404–407CrossRefGoogle Scholar
  188. Walker AW, Keasling JD (2002) Metabolic engineering of Pseudomonas putida for the utilization of parathion as a carbon and energy source. Biotechnol Bioeng 78:715–721CrossRefGoogle Scholar
  189. Wang AA, Chen W, Mulchandani A (2005) Detoxification of organophosphate nerve agents by immobilized dual functional biocatalysts in a cellulose hollow fiber bioreactor. Biotechnol Bioeng 91:379–386CrossRefGoogle Scholar
  190. Wang AJA, Mulchandani A, Chen W (2002) Specific adhesion to cellulose and hydrolysis of organophosphate nerve agents by a genetically engineered Escherichia coli strain with a surface-expressed cellulose-binding domain and organophosphorus hydrolase. Appl Environ Microbiol 68:1684–1689CrossRefGoogle Scholar
  191. Wang SJ, Loh KC (2000) New cell growth pattern on mixed substrates and substrate utilization in cometabolic transformation of 4-chlorophenol. Water Res 34:3786–3794CrossRefGoogle Scholar
  192. Wang Z, Chen S (2009) Potential of biofilm-based biofuel production. Appl Microbiol Biotechnol 83:1–18CrossRefGoogle Scholar
  193. Whiteley CG, Lee DJ (2006) Enzyme technology and biological remediation. Enzyme Microb Technol 38:291–316CrossRefGoogle Scholar
  194. Wiegel J, Zhang XM, Wu QZ (1999) Anaerobic dehalogenation of hydroxylated polychlorinated biphenyls by Desulfitobacterium dehalogenans. Appl Environ Microbiol 65:2217–2221Google Scholar
  195. Wilson L, Bouwer E (1997) Biodegradation of aromatic compounds under mixed oxygen/denitrifying conditions: a review. J Ind Microbiol Biotechnol 18:116–130CrossRefGoogle Scholar
  196. Wood T (2008) Molecular approaches in bioremediation. Curr Opin Biotechnol 19:572–578CrossRefGoogle Scholar
  197. Wu JF, Jiang CY, Wang BJ, Ma YF, Liu ZP, Liu SJ (2006) Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp strain CNB-1. Appl Environ Microbiol 72:1759–1765CrossRefGoogle Scholar
  198. Yadav JS, Reddy CA (1993) Degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) by the lignin-degrading basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 59:756–762Google Scholar
  199. Yildirim S, Franko TT, Wohlgemuth R, Kohler HPE, Witholt B, Schmid A (2005) Recombinant chlorobenzene dioxygenase from Pseudomonas sp P51: a biocatalyst for regioselective oxidation of aromatic nitriles. Adv Synth Catal 347:1060–1072CrossRefGoogle Scholar
  200. Yoem SH, Yoo YJ (1999) Removal of benzene in a hybrid bioreactor. Proc Biochem 34:281–288CrossRefGoogle Scholar
  201. Yoshiyuki O, Toshiaki K, Masataka T, Yuji N (2004) Strategies for bioremediation of polychlorinated biphenyls. Appl Microbiol Biotechnol V65:250–258Google Scholar
  202. Yu H, Kim B, Rittmann B (2001) The roles of intermediates in biodegradation of benzene, toluene, and p-xylene by Pseudomonas putida F1. Biodegradation 12:455–463CrossRefGoogle Scholar
  203. Zhang CL, Bennett GN (2005) Biodegradation of xenobiotics by anaerobic bacteria. Appl Microbiol Biotechnol 67:600–618CrossRefGoogle Scholar
  204. Zhang XM, Sullivan ER, Young LY (2000) Evidence for aromatic ring reduction in the biodegradation pathway of carboxylated naphthalene by a sulfate reducing consortium. Biodegradation 11:117–124CrossRefGoogle Scholar
  205. Zylstra G (1994) Molecular analysis of aromatic hydrocarbon degradation. In: Garte S (ed) Molecular environmental biology. Lewis Publishers, Boca RatonGoogle Scholar

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Authors and Affiliations

  1. 1.Department of Chemical and Biomolecular EngineeringNational University of SingaporeSingaporeSingapore

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